Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A4 F244 I1 R1	118	120.6	6073099	93.5%	5678347	99.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,594,376	C→T	A369T (GCA→ACA)	livM ←	branched‑chain amino acid ABC transporter permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,594,376	0	C	T	96.9%	304.2 / ‑2.2	98	A369T (GCA→ACA)	livM	branched‑chain amino acid ABC transporter permease
Reads supporting (aligned to +/- strand): ref base C (1/2); new base T (48/47); total (49/49)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 104 total aligned reads displayed.

CGCCAGATCATCATCAGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTG  >  NC_000913/3594279‑3594470

cGCCAGATCATCATCAGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTgtcg                                                                                              >  2:1171844/1‑100 (MQ=255)

 nccAGATCATCATCAGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTgtcgc                                                                                             >  2:2092348/2‑100 (MQ=255)

 gCCAGATCATCATCAGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTgtcgc                                                                                             >  1:978035/1‑100 (MQ=255)

  ccAGATCATCATCAGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTgtcgcc                                                                                            <  1:2092366/100‑1 (MQ=255)

  ccAGATCATCATCAGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTgtcgcc                                                                                            >  1:964077/1‑100 (MQ=255)

  ccAGATCATCATCAGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAACCACGCATCAACTCGCGCGACACCACCAGCAAAATTgtcgcc                                                                                            >  2:416660/1‑100 (MQ=255)

     gATCGTGATCAGCACCAGCAAACGGCCGAGCAGTAACGTGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAGATTGTCGCCa                                                                                           <  2:2395573/98‑1 (MQ=255)

     gATCATCATCAGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGa                                                                                         <  1:2855415/100‑1 (MQ=255)

      atcatcatcAGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGaa                                                                                        <  1:1661347/100‑1 (MQ=255)

       tcatcatcaGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAAt                                                                                       >  1:606492/1‑100 (MQ=255)

        catcatcaGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATc                                                                                      <  2:622821/100‑1 (MQ=255)

        catcatcaGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATc                                                                                      <  1:399722/100‑1 (MQ=255)

         atcatcaGCACCATCAAACCACTGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCa                                                                                     >  2:1612730/1‑100 (MQ=255)

         atcatcaGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCa                                                                                     >  1:2884373/1‑100 (MQ=255)

           catcaGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCAcc                                                                                   >  2:1422290/1‑100 (MQ=255)

            atcaGCACCATCAAACCACCTAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCATCAAAATTGTCGCCAGAATCACCg                                                                                  <  1:303328/100‑1 (MQ=255)

            atcaGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCg                                                                                  >  2:36181/1‑100 (MQ=255)

            atcaGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCg                                                                                  >  2:513861/1‑100 (MQ=255)

            atcaGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCg                                                                                  <  2:776940/100‑1 (MQ=255)

             tcaGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGc                                                                                 >  2:2308032/1‑100 (MQ=255)

               aGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATTACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCaa                                                                               >  2:624120/1‑100 (MQ=255)

                 cACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAAt                                                                             >  1:1923454/1‑100 (MQ=255)

                   ccATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTg                                                                           <  2:105254/100‑1 (MQ=255)

                    cATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGc                                                                          >  1:1204301/1‑100 (MQ=255)

                     aTCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCg                                                                         <  1:837414/100‑1 (MQ=255)

                      tCAAACCACCTAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCATCACAATTGTCGCCAGAATCACCGCAAATTGCGa                                                                        <  2:1990451/100‑1 (MQ=255)

                        aaaCCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGc                                                                      >  1:1773075/1‑100 (MQ=255)

                          accaccGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGccc                                                                    <  1:1272183/100‑1 (MQ=255)

                            caccGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCAt                                                                  <  2:866359/100‑1 (MQ=255)

                              ccGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATa                                                                 >  2:2711573/1‑99 (MQ=255)

                               cGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATAcc                                                               >  2:1324452/1‑100 (MQ=255)

                                  gCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATAccgcc                                                            <  1:1457334/100‑1 (MQ=255)

                                   cATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATAccgccg                                                           <  2:2994384/100‑1 (MQ=255)

                                   cATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATAccgccg                                                           >  2:784111/1‑100 (MQ=255)

                                   cATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATAccgccg                                                           <  1:1154866/100‑1 (MQ=255)

                                   cATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATAccgccg                                                           >  1:554955/1‑100 (MQ=255)

                                   cATTAACATGCTCTATTCGTTGAAATCACGCATCAACTCTCGCGACCCCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATAccgccg                                                           <  2:2290038/100‑1 (MQ=255)

                                     ttAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAg                                                         <  2:57619/100‑1 (MQ=255)

                                      tAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGc                                                        <  1:487742/100‑1 (MQ=255)

                                      tAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGc                                                        >  1:2815953/1‑100 (MQ=255)

                                       aaCATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAgga                                                       >  2:1839669/1‑98 (MQ=255)

                                       aaCATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGca                                                       >  1:1573092/1‑100 (MQ=255)

                                         cATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGcacc                                                     <  2:2494593/100‑1 (MQ=255)

                                          aTGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGcacca                                                    >  2:1198130/1‑100 (MQ=255)

                                           tGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATGGCGAGCCCATACCGCCGAGcacc                                                     >  1:120571/1‑98 (MQ=255)

                                            gCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACt                                                  <  2:2712778/100‑1 (MQ=255)

                                            gCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACt                                                  >  2:2197161/1‑100 (MQ=255)

                                               gTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATc                                               <  1:1610427/100‑1 (MQ=255)

                                                tATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCg                                              <  2:897077/100‑1 (MQ=255)

                                                tATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCg                                              <  2:2602181/100‑1 (MQ=255)

                                                 aTTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGc                                             >  2:1139892/1‑100 (MQ=255)

                                                 aTTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGc                                             >  1:489393/1‑100 (MQ=255)

                                                  ttCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGcc                                            <  2:2584870/100‑1 (MQ=255)

                                                  ttCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGcc                                            <  2:2319812/100‑1 (MQ=255)

                                                    cGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAg                                          <  2:2960718/100‑1 (MQ=255)

                                                     gTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGc                                         <  2:489388/100‑1 (MQ=255)

                                                     gTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGc                                         >  2:1149356/1‑100 (MQ=255)

                                                     gTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGc                                         <  1:513867/100‑1 (MQ=255)

                                                     gTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGc                                         >  1:2184000/1‑100 (MQ=255)

                                                     gTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGc                                         >  2:503032/1‑100 (MQ=255)

                                                       tGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGcac                                       <  2:2884347/100‑1 (MQ=255)

                                                       tGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGcac                                       >  2:282867/1‑100 (MQ=255)

                                                        gAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCTGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGcaca                                      >  2:1666341/1‑100 (MQ=255)

                                                        gAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGcaca                                      >  2:1134347/1‑100 (MQ=255)

                                                           aacACGCATCAACACGCGCGACACCACCAGCCAAATTGTCGCGAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAAc                                   >  1:2045298/3‑100 (MQ=255)

                                                           aTCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAAc                                   >  1:921914/1‑100 (MQ=255)

                                                            tCACGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACg                                  <  1:2124883/100‑1 (MQ=255)

                                                              aCGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGcc                                >  2:650971/1‑100 (MQ=255)

                                                               cGCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCg                               >  1:1065165/1‑100 (MQ=255)

                                                                gCATCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGa                              >  2:1084625/1‑100 (MQ=255)

                                                                  aTCAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGCGCACCACTATCGCCAGCACAAACGCCGAtt                            >  2:2049618/1‑100 (MQ=255)

                                                                    cAACTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCg                          >  2:1476434/1‑100 (MQ=255)

                                                                      aCTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGc                        >  2:1590783/1‑100 (MQ=255)

                                                                      aCTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGc                        <  1:1795798/100‑1 (MQ=255)

                                                                      aCTCCCCCGACACCACCAACAAAATTGCCGCCAGAATCACCGCAAATCGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGc                        <  2:1773060/100‑1 (MQ=255)

                                                                       cTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGc                        <  2:830523/99‑1 (MQ=255)

                                                                       cTCGCGCGACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCAGAGCACCACTATCGCAAGCACAAACGCCGATTCGGCa                       >  1:2187157/1‑100 (MQ=255)

                                                                          gcgcgACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCaaa                     >  2:2763165/1‑99 (MQ=255)

                                                                           cgcgACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAGCGCCGATTCGGCAAAgg                   <  1:382335/100‑1 (MQ=255)

                                                                           cgcgACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAgg                   <  2:2362454/100‑1 (MQ=255)

                                                                           cgcgACACCACCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAgg                   <  1:385632/100‑1 (MQ=255)

                                                                                caccacCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAg              <  2:1780918/100‑1 (MQ=255)

                                                                                caccacCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAg              <  2:604648/100‑1 (MQ=255)

                                                                                caccacCAGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAg              <  2:2626820/100‑1 (MQ=255)

                                                                                   caccaGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGAt           <  2:652349/100‑1 (MQ=255)

                                                                                    accaGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGAtt          >  1:2913559/1‑100 (MQ=255)

                                                                                    accaGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGAtt          >  1:871142/1‑100 (MQ=255)

                                                                                     ccaGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATAGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTc         <  2:443877/100‑1 (MQ=255)

                                                                                      caGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTcc        >  2:2161925/1‑100 (MQ=255)

                                                                                      caGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTcc        >  2:433433/1‑100 (MQ=255)

                                                                                      caGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCCATTCGGCAAAGGAGAAGGATTcc        >  2:1518016/1‑100 (MQ=255)

                                                                                       aGCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTCCg       <  2:2184795/100‑1 (MQ=255)

                                                                                        gCAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTCCgg      >  1:9427/1‑100 (MQ=255)

                                                                                         cAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTCCggg     >  1:2228071/1‑100 (MQ=255)

                                                                                         cAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTCCggg     >  1:1336465/1‑100 (MQ=255)

                                                                                         cAAAATTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTCCggg     >  1:2558345/1‑100 (MQ=255)

                                                                                          aaaaTTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGc    <  1:919331/100‑1 (MQ=255)

                                                                                           aaaTTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCt   <  2:2144386/100‑1 (MQ=255)

                                                                                            aaTTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTg  <  1:138270/100‑1 (MQ=255)

                                                                                            aaTTGTCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTg  <  2:1184229/100‑1 (MQ=255)

CGCCAGATCATCATCAGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTG  >  NC_000913/3594279‑3594470

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A